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Johansen has been indicted on three counts, as has Sierra Leone FA (SLFA) Secretary General Chris Kamara.
Both were detained last year as the ACC investigated potential abuse of funds.
Johansen has denied the charges, which come two days after she announced her intention to stand for another term.
“It’s another sad day for justice, integrity and patriotism in Sierra Leone, another sad day for any woman who dares to pioneer change. I always knew that my announcement to run for a second term would provoke strong reactions.”
ACC officials and armed police subsequently raided the SLFA secretariat in Freetown and took away computers and documents to help their investigation.
Brima Kamara has no case to answer.
“I can confirm that the SLFA President and Kamara have been indicted on six counts relating to abuse of office and misappropriation of public funds,” ACC chairman Ade Macauley said at a news conference on Thursday.
“Their first appearance in court will be on 30 October.”
Macauley told BBC Sport that the public funds include money the SLFA received from donors, with football’s world governing body Fifa among them.
Due in Freetown next week to pave the way for new SLFA elections, Fifa has previously stated it is satisfied with the body’s financial books.
Johansen took charge of the SLFA in 2013 and her reign has been blighted by controversy, infighting and the impact of the Ebola virus.
The SLFA was supposed to hold elections in early August but these were delayed by football’s world governing body Fifa until integrity checks on current and potential SLFA executive members are carried out.